[petsc-users] errors when using elemental with petsc3.10.5

Thu Aug 22 16:06:59 CDT 2019

hi, Satish,

as you have suggested, i compiled a new version using 3.11.3,
it compiles well, the errors occur in checking. i also attach
the errors of check. thanks very much,

lailai

On 8/22/19 4:16 PM, Balay, Satish wrote:
> Any reason for using  petsc-3.10.5 and not latest petsc-3.11?
>
> I suggest starting from scatch and rebuilding.
>
> And if you still have issues - send corresponding configure.log and make.log
>
> Satish
>
> On Thu, 22 Aug 2019, Lailai Zhu via petsc-users wrote:
>
>> sorry, Satish,
>>
>> but it does not seem to solve the problem.
>>
>> best,
>> lailai
>>
>> On 8/22/19 12:41 AM, Balay, Satish wrote:
>>> Can you run 'make' again and see if this error goes away?
>>>
>>> Satish
>>>
>>> On Wed, 21 Aug 2019, Lailai Zhu via petsc-users wrote:
>>>
>>>> hi, Satish,
>>>> i tried to do it following your suggestion, i get the following errors when
>>>> installing.
>>>> here is my configuration,
>>>>
>>>> any ideas?
>>>>
>>>> best,
>>>> lailai
>>>>
>>>> ./config/configure.py --with-c++-support --known-mpi-shared-libraries=1
>>>> --with-batch=0  --with-mpi=1 --with-debugging=0  CXXOPTFLAGS="-g -O3"
>>>> COPTFLAGS="-O3 -ip -axCORE-AVX2 -xSSE4.2" FOPTFLAGS="-O3 -ip -axCORE-AVX2
>>>> -xSSE4.2" --with-blas-lapack-dir=/opt/intel/mkl --download-elemental=1
>>>> --download-blacs=1  --download-scalapack=1  --download-hypre=1
>>>> --download-plapack=1 --with-cc=mpicc --with-cxx=mpic++ --with-fc=mpifort
>>>> --download-amd=1 --download-anamod=1 --download-blopex=1
>>>> --download-dscpack=1     --download-sprng=1 --download-superlu=1
>>>> --with-cxx-dialect=C++11 --download-metis --download-parmetis
>>>>
>>>>
>>>>
>>>> pet3.10.5-intel19-mpich3.3/obj/mat/impls/sbaij/seq/sbaij.o: In function
>>>> `MatCreate_SeqSBAIJ':
>>>> sbaij.c:(.text+0x1bc45): undefined reference to
>>>> `MatConvert_SeqSBAIJ_Elemental'
>>>> ld: pet3.10.5-intel19-mpich3.3/obj/mat/impls/sbaij/seq/sbaij.o: relocation
>>>> R_X86_64_PC32 against undefined hidden symbol
>>>> `MatConvert_SeqSBAIJ_Elemental'
>>>> can not be used when making a shared object
>>>> ld: final link failed: Bad value
>>>> gmakefile:86: recipe for target
>>>> 'pet3.10.5-intel19-mpich3.3/lib/libpetsc.so.3.10.5' failed
>>>> make[2]: *** [pet3.10.5-intel19-mpich3.3/lib/libpetsc.so.3.10.5] Error 1
>>>> make[2]: Leaving directory
>>>> '/usr/nonroot/petsc/petsc3.10.5_intel19_mpich3.3'
>>>> ........................../petsc3.10.5_intel19_mpich3.3/lib/petsc/conf/rules:81:
>>>> recipe for target 'gnumake' failed
>>>> make[1]: *** [gnumake] Error 2
>>>> make[1]: Leaving directory
>>>> '/usr/nonroot/petsc/petsc3.10.5_intel19_mpich3.3'
>>>> **************************ERROR*************************************
>>>>    Error during compile, check
>>>> pet3.10.5-intel19-mpich3.3/lib/petsc/conf/make.log
>>>>    Send it and pet3.10.5-intel19-mpich3.3/lib/petsc/conf/configure.log to
>>>> petsc-maint at mcs.anl.gov
>>>>
>>>> On 8/21/19 10:58 PM, Balay, Satish wrote:
>>>>> To install elemental - you use: --download-elemental=1 [not
>>>>> --download-elemental-commit=v0.87.7]
>>>>>
>>>>> Satish
>>>>>
>>>>>
>>>>> On Wed, 21 Aug 2019, Lailai Zhu via petsc-users wrote:
>>>>>
>>>>>> hi, dear petsc developers,
>>>>>>
>>>>>> I am having a problem when using the external solver elemental.
>>>>>> I installed petsc3.10.5 version with the flag
>>>>>> --download-elemental-commit=v0.87.7
>>>>>> the installation seems to be ok. However, it seems that i may not be able
>>>>>> to use the elemental solver though.
>>>>>>
>>>>>> I followed this page
>>>>>> https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MATELEMENTAL.html
>>>>>> to interface the elemental solver, namely,
>>>>>> MatSetType(A,MATELEMENTAL);
>>>>>> or set it via the command line '*-mat_type elemental*',
>>>>>>
>>>>>> in either case, i will get the following error,
>>>>>>
>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>> --------------------------------------------------------------
>>>>>> [0]PETSC ERROR: Unknown type. Check for miss-spelling or missing package:
>>>>>> http://www.mcs.anl.gov/petsc/documentation/installation.html#external
>>>>>> [0]PETSC ERROR: Unknown Mat type given: elemental
>>>>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>>>>>> for
>>>>>> trouble shooting.
>>>>>> [0]PETSC ERROR: Petsc Release Version 3.10.5, Mar, 28, 2019
>>>>>>
>>>>>> May i ask whether there will be a way or some specific petsc versions
>>>>>> that
>>>>>> are
>>>>>> able to use the elemental solver?
>>>>>>
>>>>>> Thanks in advance,
>>>>>>
>>>>>> best,
>>>>>> lailai
>>>>>>

-------------- next part --------------
Running test examples to verify correct installation
Using PETSC_DIR=/somedir/petsc3.11.3_intel19_mpich3.3 and PETSC_ARCH=pet3.11.3-intel19-mpich3.3
Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI process
See http://www.mcs.anl.gov/petsc/documentation/faq.html
./ex19: symbol lookup error: /usr/lib/libparmetis.so: undefined symbol: ompi_mpi_comm_world
Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 MPI processes
See http://www.mcs.anl.gov/petsc/documentation/faq.html
./ex19: symbol lookup error: /usr/lib/libparmetis.so: undefined symbol: ompi_mpi_comm_world
./ex19: symbol lookup error: /usr/lib/libparmetis.so: undefined symbol: ompi_mpi_comm_world
1,5c1,2
< lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
<   0 SNES Function norm 0.0406612 
<   1 SNES Function norm 4.12227e-06 
<   2 SNES Function norm 6.098e-11 
< Number of SNES iterations = 2
---
> ./ex19: symbol lookup error: /usr/lib/libparmetis.so: undefined symbol: ompi_mpi_comm_world
> ./ex19: symbol lookup error: /usr/lib/libparmetis.so: undefined symbol: ompi_mpi_comm_world
/somedir/petsc3.11.3_intel19_mpich3.3/src/snes/examples/tutorials
Possible problem with ex19 running with hypre, diffs above
=========================================
Possible error running Fortran example src/snes/examples/tutorials/ex5f with 1 MPI process
See http://www.mcs.anl.gov/petsc/documentation/faq.html
./ex5f: symbol lookup error: /usr/lib/libparmetis.so: undefined symbol: ompi_mpi_comm_world
Completed test examples
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